Interaction with the core LDMAP binary, `ldmapper1` is most user friendly through the shell wrapper script `ldmap`. Running `ldmap` brings up the following menu:
1 Construct LD map in segments from intermediate file
2 quit
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The wrapper script `ldmap` works by requesting parameters from the user, and writing a small executable job files (`.cp`), which then runs `ldmapper1` with these desired parameters when executed. If automation of processes is desired, the required commands may be entered into a `.cp` file directly. An example `.cp` file may look like:
`./ldmapper1 input.tped int job example.map example.log 0.05 0.001`
where `int` is a temporary file used in LD map generation, `job` is a file containing run parameters (eponymous file included with source code), `example.map` will contain the final LD map, and `example.log` will contain detailed run information, `0.05` is the desired AF cutoff, and `0.001` is the desired HWE cutoff.
`[intermediate.txt]` is an intermediate file that will be created;\
`[job]` is an existing file containing run parameters (included, does not generally need edits);\
`[out.ldmap]` will be created and contain the final LD map;\
`[out.log]` will be created and contain detailed run information;\
`[MAF]` is the desired minor allele frequency cutoff (suggest 0.05);\
`[HWE]` is the desired Hardy-Weinberg equilibrium deviation p-value cutoff (Suggest 0.001).
